Evangelion Seed
by animefan29
Summary: Shinji and Rei are Coordinators. Auska is a Natural. The arrival of the Angels stop a war. But for how long? Eva/Gundam Seed crossover.
1. Chapter 1

**Evangelion Seed**

**Disclaimer:** Anyone who owned both Evangelion and Gundam would be very wealthy. So it can't be me. But a guy can dream

"Hello" – Talking

"_Hello_" – Radio

'_Hello_' – Thoughts

**Author's Notes:** This is a fic I was challenged to write by Tellemicus Sundance. He wanted to see what I could do if I combined the worlds of Evangelion and Gundam. I am taking a number of liberties with technological advancement and history so that everything is set up by the appropriate time frame. If anyone considers anything I write here real, then I would like to see your history homework, I could use a good laugh.

* * *

**Chapter 1: Prologue**

The year 1945. A year that was many things for many people.

It was a year of celebration for the Allied forces as they broke the Axis' power and their victory was cemented with the death of Mussolini and Hitler.

It was also a year of horror and fear as the world witnessed the destruction reaped in Japan sowed by the atomic bombs that wiped Hiroshima and Nagasaki from the face of the Earth.

But for the scientific genius George Glenn, a scientist that advanced computer technology by decades, it was a year of triumph as he discovered a process that would genetically enhance humans before they were born.

* * *

In September of the year 1951 the island nation of Japan formalized its surrender by signing the Treaty of Peace.

Over fifty countries participated in the ceremony, the majority of who were disgruntled with the slap on the wrist they felt the Americans were administering to the Japanese as punishment.

Although the Japanese did pay compensation for their actions in the war, the European and Asian Allies felt that it was inadequate.

Another sore point with them was how Japan did not really lose any territory for its transgressions. Instead certain overseas territory was placed in trusteeship with the U.S. until the time America felt it was right to turn control back over to the Japanese.

In October of the same year George Glenn revealed to the world the fruit of his labor. That fruit were fifty 5 year old children, fifty 4 year olds, one-hundred 3 year olds, one-hundred 2 year olds, and two-hundred 1 year olds he had genetically enhanced. He called these children Coordinators.

Backed by the American government Glenn continued his research in the public eye. For ten years the world watched as the Coordinators, the 500 original and all subsequent groups that were born proved to have a learning curve several degrees higher then newly termed Natural children, capable of completing current high school and college course work by the time they were fifteen. The Coordinators impressed the world further with their incredible physical prowess, whether it was their hand-eye coordination, their physical speed and strength, or their natural immunity to diseases such as influenza or even the common chicken pox.

The world's view was split into three different divisions. Some saw what the Coordinators could do and didn't really care, seeing them only as the kind of people you hear about on the news but will never meet in real life. Many looked at the Coordinators with reverence, considering Glenn's work to be a medical, genetic, and technological miracle.

But many saw the results of Glenn's work and declared whether openly or quietly that the children should have never existed in the first place and that all research into human genetic manipulation should be halted and destroyed. The most vocal proponents of this view are Blue Cosmos, a French environmentalist group that was steamrolling into the political area and gaining considerable headway.

Despite the naysayers, by the year 1961 Glenn considered his work complete. With that announcement the American government, the greatest supporters of the Coordinator project, proclaimed that they would be making the technology needed to create Coordinators available to anyone who desired it. This extended to foreign countries.

In the political arena the U.S. had been having both major successes and disastrous fallouts, and it all stemmed from the issues concerning Coordinators. America found itself at odds with the other four members who formed the major Allies during World War II. Relations with Great Britain, which had finally started to progress forward after the First World War, had ground to a halt. France who had been a long time friend and ally cut off all relations and kicked out all American diplomatic entities when they were offered the technology. The Soviet Union wasn't even offered the technology considering the rivalry that existed between them and America at the time. China was in a similar boat and already had poor relations. But what truly surprised the U.S. was how they received similar reactions in most of the European, African, South American countries, Middle East, and other Asian countries.

While the 'Old World' turned back America's offer with violent words and threats, many of the 'New World' countries such as Australia, Canada, and Mexico, and older allied Asian nations such as Japan and South Korea accepted the gift with open arms and friendly gestures. However when these other eleven sovereign nations accepted it, they were put into a similar political situation as the U.S.

Following the availability of genetic manipulation technology was the Coordinator Rush. A stampede of couples wishing to have a child desired to make their children Coordinators. These people saw the genetic enhancement has the best way to ensure that their children a better future, which is the basis of all parents hopes and dreams.

While the civilians sought to improve their children, the political leaders sought ways to improve their situation with the rest of the world. All twelve nations were at a diplomatic standstill with the majority of the world, and rather slow with those who had yet to take a side in the conflict. And there was no covering up the fact that they were in a conflict similar to the Cold War that existed between the U.S. and the Soviet Union. Although everyone doubted that it would escalate into actual war, the possible repercussions did not bode well for them.

The solution that they were presented to the problem came from the Japanese who took a page from the man who once said 'United against a common enemy.' Their solution was considered radical and crazy by all whether they were conservative, moderates, or liberals. But in the end they all agreed that it was the best solution.

By early 1963 the twelve governments signed the Zodiac Alliance of Freedom Treaty, and took the name of their founding document as the name of their new super nation, which became more commonly known as ZAFT. The new government created for the new nation was crafted and erected quickly as most of its predecessors had considerable experience setting up a new political structure in a short amount of time. Although they did not have a state system like the U.S. did, they still kept the regional names of territories for practical purposes.

This action did not go unnoticed. A counter move lead by the European nations, many of whom maintained control and ties in their old colonies swiftly established an alliance between the majority of European, African, and South American countries. The alliance then quickly coalesced into the Atlantic Federation. Although the countries that formed the Federation were still separate entities, they worked as one unit and were considered a single country. The infrastructure for the Atlantic Federation's government took a considerable more time than ZAFT's as they were basing theirs off considerably older governments that were slow to change.

The sudden shift in the world political structure left the Earth with two new super powers that eclipsed the former two. Although the Soviet Union did not lose any power with the creation of the Atlantic Federation and ZAFT, their influence was no longer great enough for them to be considered a super power.

With the new super powers came a new race of economic, political, and technological power. Although ZAFT did not have much political influence outside the voice they were given in the United Nations they did develop a technological advantage thanks to projects spearheaded by the aging George Glenn and the Coordinators. The greatest example of which was the mass driver developed and built in Mexico that replaced all work concerning space travel based on chemical reaction propulsion.

In 1975 the space race had reached new heights. A handful of mass drivers had been built around the world and were being used to continually launch construction modules into space to be used in the construction of L group space colonies and orbital military bases.

In 1990 the country of North Korea sure that because of the now official Cold War between ZAFT and the Atlantic Federation there would be no retaliation launched a second invasion into the sparsely defended ZAFT territory of South Korea. Taking a page from Nazi Germany's book they struck quickly with hammer blows that broke through the unprepared defenses, ignoring and bypassing the majority of the military forces in order to reach their target. Victory seemed assured for North Korea as they closed in on Seoul, until they crossed into a military testing facility. There the North Korean army discovered ZAFT's new experimental weapon. The mobile suit OZ–06MS Leo.

Although the Leo was slow and awkward compared to many modern weapons, its versatility and firepower quickly proved it to be superior to tanks and other current military weapons. A mere handful of squads quickly turned back the invading forces and backed up by the ZAFT military forces that were ignored by the invading army, drove into North Korea. After a mere month of combat North Korea officially surrendered and was annexed into South Korea to form a single Korean territory as a part of ZAFT.

With the success of the mobile suit prototypes new attention is brought to ZAFT.

Communist China and the Soviet Union, afraid for the continued existence of everything they had built since World War II with the revelation of ZAFT's increasing military might, began a series of diplomatic discussions and treaties with each other and several other countries from the Middle East such as Kazakhstan, Mongolia, Uzbekistan, Kyrgyzstan, Turkmenistan, Iran, and Iraq. These treaties would eventually lead to the forming of the third super nation of the Eurasian Federation by 1995; however because of the differences between the governments of its constituents it would be many years before they became a unified force, experiencing the rise of several terrorist groups that opposed the union.

The UN, concerned about the possibilities of war, issued a decree stating that all current civilian space colonies, the majority of which were asteroid mining facilities, research labs, and production facilities, were to be placed under the control of the Orb Union. A chain of islands colonized in the late 1700's that had recently been gaining considerable power despite the rise of the super nations. Orb had stayed neutral in every war to take place since it was first established as a country, and was considered to be the only nation that would stay neutral if war broke out between ZAFT and the Atlantic Federation.

The purpose of the act was to make sure neither side in the Cold War could use the colonies as staging platforms for invasion armies, or as launch pads for missiles. However all nations retained control over any military bases they built in space as long as they kept to UN guidelines.

Over the following years no major incidents occurred until the year 2000 in the month of September when the Katsuragi Expedition, a team of civilian scientists from ZAFT backed by the UN, arrived in Antarctica to conduct classified research on an alien organism codenamed "Adam." And the world was forever changed on September 13 during a contact experiment with Adam awoke the creature releasing its long dormant power and causing what came to be known as Second Impact.

The only survivors of the Katsuragi Expedition were Gendo Ikari who had left Antarctica the previous day, and Misato Katsuragi daughter of Dr. Katsuragi who was found almost a day later in an emergency survival pod floating in the ocean.

The force of the explosion tilted the Earth off its axis and melted the southern ice cap, flooding the world. The sudden rise in water levels created devastating floods, tidal waves, and tsunamis that destroyed many coastal areas.

In the end the natural disasters caused by Second Impact were just the precursors of the death and destruction seen in the short yet brutal wars that followed.

But in those few months the most life changing event happened after Japan felt the effects of a third nuclear bomb that destroyed much of Tokyo killing half a million people. The bomb was deployed by the Atlantic Federation who believed Second Impact was the result of some new ZAFT weapon. In retaliation ZAFT unleashed one of its latest technological developments onto the world, the Neutron Jammer.

ZAFT launched a countless number of these devices from their satellites in orbit, driving them deep into the Earth's crust. Once activated the N-Jammers arrested the movement of free neutrons thus preventing the use of nuclear fission based technologies. This made the use of nuclear based weapons impossible and forced all active nuclear power plants to shut down. An insignificant loss to the Zodiac Alliance who had long since prepared in case they ever did use the N-Jammers.

Because of the N-Jammer field's side effect of disrupting radio waves the range of radar and all conventional forms of communication were restricted. And because of the effective range of a single N-Jammer's field it would take decades if not centuries to remove enough of them to restore the use of nuclear power and radio waves.

What followed was a series of small yet bloody battles between the Zodiac Alliance and the Atlantic Federation. It was clear that the Cold War was over and that it had been replaced by a hot one. The war would have continued and escalated if not for the intervention of the UN revealing to government leaders what Second Impact truly was and the danger that was to come. An immediate ceasefire was called and the Valentine Ceasefire signed on February 14 of 2001 AD. On that same day a new calendar was established, naming the day the treaty was signed as February 14 of 1 CE or Cosmic Era.

In order to prevent panic about the situation the "official" explanation for Second Impact was that a meteorite 10 centimeters wide and traveling at 95 percent of the speed of light struck Antarctica

Over the following three years Gehirn, a top-secret agency not affiliated with any government, was established to study the data gathered by the Katsuragi Expedition to develop effective countermeasures against the Angels. Their research quickly led to the development of the Evangelion and Magi super-computers. The organization would be overseen by the Instrumentality Committee, a group of five UN appointed officials that would report anything and everything to the 'leaders' of the UN.

During this same time period there was a significant amount of immigration to the Orb Union and into space.

The Orb Union despite being a chain of islands, was relatively unaffected by the rising water levels due to how unusually high the islands reached above sea level. Their tropical paradise climate only added to the allure. But what truly brought people in was how moderately minded Orb was and their laws that not only kept them neutral in all global affairs but prevented the persecution of any person whether they were a Natural or a Coordinator, making the place a haven to those tired of the radicalist way of thinking in AF or the isolationist ways ZAFT had been adopting.

Granted ZAFT had a similar policy, but some of its residents had grown tired of the hostilities they shared with the AF which was growing more Blue Cosmos minded with each passing year.

Space was also an attractive alternative too many people after Second Impact forever changed the Earth. Each year thousands of people flew to space in order to get a job working on either the S group colonies being built by the Atlantic Federation and Eurasian Federation, or the PLANTs (Productive Location Ally on Nexus Technology) under ZAFT construction.

The UN had allowed other nations besides Orb to build and own civilian colonies as a part of their territory as long as they followed specified guidelines. Guidelines such as not being used to build or store military weapons or warships, being kept in a sanctioned geo-synchronous orbit around the Earth, and kept at a distance where they could pose no military threat to the Earth.

But despite the ceasefire and the fact the most of the Earth was currently working towards a common goal tensions between the nations of the world remained high.

In the Atlantic Federation as each year went by more and more of its leaders were unofficially accepting the policies of Blue Cosmos for their own.

The Eurasian Federation, while not as radically minded as its Atlantic counterpart, was not particularly fond of either ZAFT or the AF. ZAFT was just the bigger threat in their mind, so should the war start up again their allegiance would go to the Atlantic Federation.

The Zodiac Alliance felt the same as the other two super-power nations. However unlike them, with its recent and somewhat forced isolationist policies ZAFT had only a few trading partners beyond its borders, the largest of which was Orb, and none of them were willing to get dragged into a war amongst the super-powers. Instead the nation would have to rely more on its technology to create a mobile suite standard army.

So the leaders of each one of the super-powers began preparations for the continuation of the war once the coming Angels were defeated…if they were defeated…if they came at all.

However not everyone was so desperate for war and bloodshed. Over the years a number of political figures attempted to mend the bridge between the three nations, and if their clearance was high enough often through Gehirn. That is until 10 CE when Gehirn is disbanded with all personnel, assets, and facilities being transferred to NERV, an organization run by Gendo Ikari and overseen by the UN's Instrumentality Committee. Its purpose is to continue Gehirn's research and to use it in defense against the Angels, no longer allowing any civilians not associated with NERV from using or even being allowed within their facilities.

But despite this setback some people would not be denied in their goal. None more so then Lenore Zala, wife to Patrick Zala a swiftly rising political figure in ZAFT. She was a woman of grace, beauty, and a gentle disposition making her a beloved icon for peace in the Zodiac Alliance.

Many in the world believed that if anyone had the persistence and determination to truly end the war that had been on a temporary truce for more than a decade and bring true peace to the world it was her.

Lenore never gave up even when the ceasefire was ended on February 11, 14 CE after a terrorist attack on February 5 destroyed the United Nations that had been relocated onto the moon several years prior, and the majority of the current UN leadership was killed. Evidence was found that could be used to link just about any nation as the one responsible for the attack.

Alas, it is sad and heartbreaking to know that if Lenore's dreams were ever realized that she herself would never get a chance to see it. Because on February 14 of 14 CE, several days before she was to meet and discuss possible peace treaties with Atlantic and Eurasian Federation representatives, Lenore Zala was killed in the destruction of the Junius 7, one of the newest of ZAFT's PLANTs to be constructed. An event that became known as the Bloody Valentine Incident.

The cause of the destruction was a nuclear missile, the fourth used in history, fired from one of the Atlantic Federation mobile armors that had been in the area legally as part of an AF task force.

ZAFT citizens howled for revenge at the loss of not only one of their most beloved icons but for the thousands of innocent civilians that perished in the colony's destruction.

This was the act that truly rekindled the war that had been put on hold 14 years earlier. Using their technologically superior mobile suits ZAFT launched several invasion forces into Southeast Asia, Central America, and Northern Africa.

Both the Atlantic Federation and Eurasian Federation leaders made the same declaration as their ZAFT counterparts and to counteract the invasions joined together in a military alliance along with several others of their allies. This alliance became more formally known as the Earth Alliance, because of the sheer number of countries that were involved, and their combined military forces became known as OMNI Enforcer (Oppose Militancy and Neutralize Invasion).

The Earth Alliance met ZAFT in the field of battle, hoping to use their superior numbers to crush the ZAFT military. However it quickly became apparent that despite being vastly outnumbered ZAFT mobile suits were more than a match for their OMNI opponents.

This was particularly obvious in space where the ZGMF-1017 GINN mobile suit proved tactically superior to the Earth Alliance's TS-MA2 Moebius mobile armor, the EA often needing five Moebius to bring down a single GINN.

In an attempt to turn the tides of war the Earth Alliance turned to the G Project spearheaded by the Atlantic Federation. The purpose of the G Project, which began several years prior, was to create a series of prototype mobile suits that would be able to fight on par with anything ZAFT fielded yet could hopefully be piloted by Naturals.

To ensure secrecy the Atlantic Federation worked with Morgenroete, a military contractor based in the Orb Union. Specifically within its facilities in the Orb colony Heliopolis.

However ZAFT caught wind of the project as it was nearing completion. In an act unsanctioned by the ZAFT Supreme Council, the Rau Le Creuset team infiltrated Heliopolis, destroyed the Morgenroete facilities, attempted to destroy the new warship the _Archangel_, and managed to steal 4 of the 5 G Weapons.

The final suit, the GAT-X105 Strike, remained in Alliance hands. But due to the circumstances of battle ended up being piloted by Kira Yamato, a young Coordinator and citizen of Orb who completed the mobile suit's unfinished operating system but configured it to Coordinator use. During the battle Heliopolis was destroyed by a combination of Rau Le Creuset ordering the GINN's under his command to use D-type heavy weapons, and Kira underestimating how powerful the Strike's weapons were. Fortunately there were no casualties among the Orb civilians who had time to evacuate into the shelters that acted as life boats in case of the colony's destruction, several of which were brought aboard the _Archangel_.

The _Archangel_ fled the destruction of Heliopolis pursued by ZAFT warships under Rau Le Creuset's command who sought to capture or destroy the Strike and destroy the _Archangel_.

With the Bloody Valentine War raging across the Earth and Heavens NERV and its purpose were almost forgotten. Almost.

* * *

 Evan Wilson, captain of the _Vosgulov_-class submarine _Varnass_, did his best to stifle a yawn, not being entirely successful. He stood aboard the bridge of his vessel and it would not do to show the men under his command how tired he was. But the fact of the matter was he was bored.

The war had been going on for nearly a year now and over the past eleven months he and the _Varnass_ had served with distinction in the Indian Ocean against the Atlantic Federation Navy operating off the coast of Africa. There were even a few rumors that he could end up being promoted to Commander. That was until a month ago when he and several other captains had been reassigned.

Now here he was patrolling the middle of the Pacific Ocean smack dab in the middle of ZAFT territory. If it weren't for the possible threat of the Eurasian Federation attacking from the Northwest or the Atlantic Federation attacking from the Southeast then there would be no point for any warship to be here. But those threats were minor considering how most of the Earth Alliance Navy in those areas were pinned closer to shore, unless one managed to slip out. Otherwise out here only a few hundred miles away from Hawaii the only company they had were the fishes.

Captain Wilson suppressed the urge to sigh as he wondered for the thousandth time what he had done to be punished this way. His standing orders were to patrol for and investigate any anomalies in the Pacific Ocean. The orders were vague and for an indefinite period of time. The kind that usually meant the end of a man's career.

He might have continued his ponderings if he hadn't been interrupted by one of his subordinates. "Captain." Called the soldier manning the sonar. "I'm picking up a large unidentified object on sonar moving at a steady pace beneath the surface."

"Is it one of ours?" Asked Captain Wilson.

"Negative. It's too small to be a sub and too large to be a mobile suit. Also too quite to be propelled by engines."

"Probably just a whale then." Dismissed the captain.

"Negative. Too big to be a whale and possibly even quieter."

Wilson frowned. If it was bigger than a whale then it had to be man-made. But to move quieter then a whale made it something that he had never heard of. And just the sort of anomaly he had been searching for. "Launch two GOOhNs and get us within visual range. I want to see what this thing is." He ordered.

The _Varnass _moved in on the unknown object with its GOOhN escort several dozen meters ahead.

"_Sir,_" said one of the of the GOOhN pilots over the radio. "We have a visual of the target."

"What do you see?"

"To be honest sir we have no idea." Admitted the pilot. "At first glance I would say some sort of mobile suit. But the longer I look at it the less likely that seems."

"Are we in visual range yet?" Asked Wilson

"Yes sir."

"Put it on screen."

One of the monitors turned on to show the view seen by one of the outside cameras. What it showed easily explained the pilot's words. Whatever the thing was it had a vaguely humanoid shape like a mobile suit, but that's where the similarities ended. Twice the size of the GOOhNs with long spindly arms and legs. Bony protrusions were visible along its shoulders and sides. And from the current angle nothing in the way of a head could be discerned.

"What's its current velocity?"

"If its course doesn't change it will reach the shores of Japan in eight hours." Was the response.

"Alright if the N-Jammers aren't interfering with our radio too badly then I want to hail this thing. If it doesn't respond then we are to assume it is of hostile intent." Wilson ordered.

"Yes sir. Hailing now."

Picking up the radio the Captain Wilson attempted to make contact with the unknown. "Hailing unknown vessel. This is the _Varnass_, please respond and identify yourself." Silence was the only thing that responded to him. "Unknown vessel, you are within ZAFT territorial waters. Respond and identify yourself or else we will have no choice but to open fire." Again there was no return signal. "Unknown vessel this is your last warning. If you do not respond we will open fire." Nothing. "Tell the GOOhNs to launch torpedoes." He ordered.

Lifting their arms the aquatic mobile suits launched a barrage of 14 torpedoes each from their arm mounted torpedo launchers. The torpedoes zoomed in on the unidentified object, exploding upon impact against the things side.

Captain Wilson smiled. 28 torpedoes were a little excessive for a single target of such size. But when dealing with the unknown it was better to err on the side of caution. "Target's status?" He asked the individual watching the sonar.

The soldier looked at his monitor and paled. "Target is continuing its course. No change."

"What!" Exclaimed the captain. Turning back to the monitor he watched as the water calmed and visibility returned to reveal a perfectly intact…whatever the hell it is. "Have the GOOhNs back off. Arm all torpedoes tubes. Once the mobile suits are out of range fire all torpedoes."

After the GOOhNs had moved away the _Varnass_ fired twelve of it more powerful torpedoes. Just like before they exploded against the thing. And just like before the target wasn't damaged.

"Has there been any change at all?" Wilson asked keeping the desperation from his voice.

"Target's course and speed have not been altered. There is no discernable damage to target's exterior." Came the stunned report.

"Send the GOOhNs back in. I want to know what this thing is and why we can't hurt it."

Following the captain's orders the mobile suits swam forward and started circling around the rather ugly monstrosity.

Seeming to grow annoyed with the two smaller machines the target lifted its arms unleashing energy lances that sliced the two GOOhNs in half.

"Sir! Target has responded! It's destroyed both mobile suits!" Exclaimed one of the crewmen.

"Status of the pilots!?"

"Their dead sir." Was the grim response

"Damn it." Cursed the captain. "Helmsman I want us brought to the surface. I want the rest of our GOOhNs in the water. I want the DINNs in the air on their way to Japan. We're going to use everything we've got to stop this thing. And if we can't then at least the military will have an early warning about this…monstrosity." The crewmen rushed to do their jobs, arming weapons, getting pilots to their mobile suits, and raising the _Varnass_ to the surface to launch the DINNs.

Whatever this thing was they were going to make sure it was stopped, one way or another.

* * *

As man met the first angel to appear in 15 years, a different encounter was happening in space.

A confrontation between three warships, two advanced mobile suits, and two childhood friends. On one side lies the _Archangel_, the most advanced and powerful warship created by man, its aft weapons armed and ready to fire on the ZAFT ships that had until moments ago had been pursuing them.

Said ships, the _Nazca_-class Destroyer _Vesalius_ and the _Laurasia_-class Frigate _Gamow_, waited with their own weapons shut down and engines on standby.

Between them were two mobile suits. The captured X303 Aegis, piloted by Athrun Zala, and the X105 Strike mere meters apart with the Strike keeping its beam rifle trained on the red mobile suit. The cockpit hatches were open allowing Kira and Athrun to perfectly see each other. Between the two, floating towards the Aegis was Lacus Clyne whom Kira had gone to great trouble to get off the _Archangel_ and was probably going to be sent to the brig for this.

But he had to do what he thought was right. And keeping a gentle soul like Ms. Clyne prisoner aboard the _Archangel_ where she was being used as a hostage was not something he could allow. None of the crew had liked the situation in fact most of them hated using her that way, except maybe Ensign Badgiruel who more easily accepted it since it kept the ZAFT forces from attacking. But it was still wrong and unlike the others Kira couldn't be court marshaled.

As Lacus reached the Aegis she was caught by her fiancé Athrun who spent a few seconds looking at the bulge in her space suit where her clothes were hidden while she thanked the pilot of the Strike for what he had done. With Lacus safe in his arms Athrun turned and called out to his old friend Kira. "Kira! Come with me too." He said a little to Kira's surprise at the offer. "Is there any reason for you to remain in the Earth Alliance?"

"I'm sorry Athrun." Called back Kira struggling through the words, knowing what saying them means. "I don't want to fight you, but my friends are on that ship and I'll do whatever I must to protect them."

"If that's the case Kira, then the next time we do battle I will fire at you!" Stated Athrun, holding back the tears that those words wanted to create.

"And so will I!" Responded Kira. "I just wish that it didn't have to be this way." He said more quietly, just barely loud enough for the two across from him to hear. The cockpit of his mobile suit closed and the Strike started drifting back to the Archangel.

Aboard the _Vesalius_ Captain Aides reported what was happening to Commander Le Creuset. "Enemy mobile suit is increasing in distance."

"_Very well_." Said the Commander aboard his CGUE in the mobile suit hanger. "_Start the engines, Aides_!"

The Captain was about to give the command when his communications officer spoke up. "Sir! We are picking up an open message being transmitted on all military frequencies! It says that the ceasefire is back in effect and for all hostile actions to cease!"

"What?" Exclaimed the Captain. "Can you confirm the transmission's origins?"

"Doing that now sir…We have confirmation. The transmission is a legitimate announcement from the Supreme Council and is also being transmitted on all civilian bands as well."

"_What's going Captain?_" Asked Le Creuset wondering why the vessel had yet to move or why he hadn't been launched yet.

"Commander, the Supreme Council has just announced that the ceasefire is back in effect."

"_Does the Supreme Council give a reason?_"

Turning to his communications officer for the answer, the young mad said. "The transmission to the military says that it has to do with a Code: Angel."

"_I see, so the time has finally come._"

"Sir?" Queried Aides, unsure as to what the Commander was talking about.

"_I'm returning to the bridge Captain. And hail the Legged Ship. I am going to want to talk to their Commander._"

"Yes sir." Responded Aides.

Meanwhile aboard the _Archangel_ Lt. Murrue Ramius was being given similar message from the communication operator Kuzzey Buskirk.

"Are you sure?" She asked.

"Positive." Said the civilian operator. "The message has the Earth Alliance's current authenticity codes and is being accompanied something called a Code: Angel."

Murrue gasped. She had spent time at NERV Germany and knew precisely what a Code: Angel meant. However before she could respond Kuzzey spoke up again. "Ma'am we are being hailed by the _Nazca_-class."

"Put it on screen." Murrue ordered.

On the main communication appeared the image of the famed masked Commander and mobile suit ace of ZAFT. "_This is Commander Rau Le Creuset. I wish to speak with the Commander of the Legged Ship about the ceasefire and of a possible alliance._"

Murrue looked a little surprised when he said alliance but quickly hid it. "This is Lt. Murrue Ramius, Captain of the _Archangel_. What is it you wish to say?"

"_Assuming you have received the same message as we have, then I wish to inquire as to whether anyone aboard your ship was familiar with Code: Angel. It has been 15 years since the code was first created, and probably 5 years since anyone has given it some serious thought._"

"Yes Commander Le Creuset." Responded Murrue. "I was stationed as NERV Germany 4 years ago as an AF liaison. A Code: Angel means that the Angels have appeared." The bridge crew glanced around each other trying to see if that comment made any sense to any of the others. From the looks of it no.

"_Correct Lt. Ramius. Right now defenses are being prepared at wherever this new Angel is headed, which is suspected to be towards the 1__st__ Branch of NERV in Japan. And as I am sure you know NERV believes that conventional weapons will have little if any effect on them._"

"And what does that have to do with an alliance?" Asked Murrue.

Le Creuset smiled softly as he laid out his plan. "_Because when they designated conventional weapons, NERV was referring to projectile weapons such as guns and missiles. By that definition the G-Series mobile suits are all equipped with unconventional weapons._"

"Their beam weaponry?" Murrue hazarded a guess. "But what about the weapons NERV has been developing?" While she had worked in a NERV base for a while she never had the clearance to know everything that they were doing.

"_From what I understand NERV's weapons have never been field tested meaning that while they were designed to be used against the Angels there is no guarantee that they will succeed. Granted the same could be said for the G-Weapons when facing an Angel, but I have a feeling that things will go much more smoothly if they grace the battlefield with their presence._"

"Captain," whispered Natarle next to Murrue. "You can't possibly be considering this proposal. They're ZAFT. And our orders say to meet up with the 8th fleet"

"Ensign Badgiruel, do you know what will happen if even one Angel reaches its objective?" Asked the acting Captain. Natarle shook her head. "There will be a Third Impact." Numerous people around the bridge gasped most of them were old enough to remember what happened during Second Impact and they all knew that it was doubtful that the world could survive another.

Turning back to the monitor Lt. Ramius agreed to an alliance.

Rau just smiled and said, "Wonderful."

* * *

Several hours later found Kira in the cockpit of the Strike. He was currently updating the Strike's OS so it could more easily move while under the effects of Earth's gravity.

Kira would be the first to admit that he was probably one of the last people who would one to spend his time preparing for a battle. But it beat doing whatever punishment the _Archangel's_ XO had planned for him. And his mood was improved further by the sight of mobile suit on the opposing wall of the hanger.

After the ceasefire had called (again) the command staff of the _Archangel_ and the Le Creuset team discussed a plan of what needed to be done. Lt. Ramius and Commander Le Creuset had both been adamant that despite any standing orders they had to get down to Earth and help in the fight against something called an Angel. Ensign Badgiruel insisted that it was top priority for the _Archangel_ to join with the 8th fleet. Commander La Flaga was up in the air about it. Until a video image was broadcast over ZAFT's military bands showing the first conflict against the Angel.

The way the monster shrugged off multiple torpedo volleys and then destroyed the GOOhNs has if it were swatting at bugs had quickly changed their minds.

Their decided plan was first to transfer all of the Gundams over to the _Archangel_. Now Athrun's Aegis shared the right hanger with Kira's Strike and Mu's Moebius Zero, and in the previously empty left hanger now contained the GAT-X102 Duel, GAT-X103 Buster, and the GAT-X207 Blitz. Kira was glad that the civilians had been taken off the ship and shuttled over to the ZAFT vessels during that time so they wouldn't be in danger. The second was to reach a point over the Earth where the _Archangel_ could descend to an intercept point between the Angel and Tokyo-3, the suspected target. Finally once they had reached the Angel the _Archangel_ would engage it while the Gundams disembarked to engage it as well.

Originally Commander Le Creuset had wanted to put the Strike and Aegis aboard the _Gamow_ and then detach the hanger using its capabilities as an atmospheric re-entry capsule. However Murrue quickly shot that down when she informed him that _Archangel_ was capable of atmospheric re-entry itself. It was only logical that the captured ZAFT suits should be brought over to the ship that was originally built to support them in combat, was fully equipped to house and repair them, and had a crew trained specifically for that job.

Rau couldn't argue against such a well prepared argument.

Currently the scheduled atmospheric re-entry was to happen in just one hour. By current estimations they should be able to engage the Angel shortly after it made landfall.

Pausing in his typing for a moment Kira couldn't help but contemplate the irony. He had wished that there was some way that he would no longer have to fight Athrun and lo and behold and Angel causes a ceasefire and a temporary alliance between the _Archangel_ and the Le Creuset team. It was enough to make an atheist find religion.

Although he found he wasn't quite as fond of most of Athrun's teammates when the five of them had met briefly. Sure Nicol Amalfi, the pilot of the Blitz had been a likable enough fellow who had greeted Kira kindly despite being enemies just hours prior. But Dearka Elsman, pilot of the Buster, and Yzak Joule, of the Duel, had been less receptive of him.

They were rather upset that a Coordinator was working with the Earth Alliance. Yzak seemed especially irritated when he found out that Kira had no previous training in piloting a mobile suit when he first got into the Strike's cockpit. The only bit of mollification to the two pilots was that it hadn't been some Atlantic Federation pilot with a Natural use OS, which was a closely guarded secret in ZAFT.

Kira sighed hoping that their current feelings wouldn't have an adverse on the upcoming confrontation.

Looking around he took in the faces of all the techs and crewmen prepping the ship and mobile suits for the battle. Kira couldn't help but notice how young so many of them were. Not as young as he and the other pilots but Chief Murdoch was easily the oldest followed by Commander Mu La Flaga.

That sight made some words that Murdoch once told him come to mind. "_War is always an ugly business. And it's always made worse when I have to watch promising young men fly out in their machines only to not return._"

Kira hadn't seen nearly as much as the Chief had, but what he had seen had convinced him that at 16 he was too young for war. But as long as he could make a difference he would fight. He just hoped that nobody younger would have to know what the frontline of war was like.

* * *

Aboard a maglev train inbound to Tokyo-2 sat a young Coordinator by the name of Shinji Ikari. His full attention was upon the letter in his hand. The letter had come from his father whom Shinji hadn't even seen much less spoken to in years. The sheet of paper had only one word, "Come."

* * *

**Author's Notes: **I am probably stretching myself thin with this story. But when I was challenged by Tellemicus (a great author himself) I just couldn't say no. Granted it took a few months because I got a little bored rewriting history. Oddly enough it was watching Code Geass that got me interested again. Mecha anime, you gotta love'em. Heck I even sort of want to write one of those now. Although considering what is already on my plate I probably shouldn't, but I said the same thing about the last three stories I posted and I even have another in the works so who know.

Let me know what you people think of this story.

**Please Read and Review.**


	2. Its name is Eva

**Evangelion Seed**

**Disclaimer:** Anyone who owned both Evangelion and Gundam would be very wealthy. So it can't be me. But a guy can dream

"Hello" – Talking

"_Hello_" – Radio

'_Hello_' – Thoughts

* * *

**Chapter 2**

**February 11, 15 C.E. **

The sun was high in the sky over the shores of Japan, and would've been shining on the rubble of a city partially submerged and destroyed by Second Impact had it not been for the effort of the government to clean it up.

Metal glinted in the light as machines of war moved into position.

The road by the coast was lined with mobile assault vehicles. Specifically they are the TFA-2 ZuOOT mobile suit in tank form; a model that, while not as effective as the ZGMF-1017 GINN, had far more firepower then any counterpart used in the EA. And patrolling the skies were ZAFT combat helicopters, keeping an eye out for the expected enemy.

But these were merely the first line of defense.

Scattered behind the road stood several squads of GINNs, the second line of defense. Many were equipped with the standard MA-M3 heavy sword and MMI-M8A3 76mm heavy assault machinegun. But just as many of the pilots had decided to switch out their machine's assault machinegun in favor of the M68 Cattus 500mm recoilless rifle or even the M69 Barrus heavy ion cannon.

A single squad of Assault GINNs stood near the front, their heavy armor and assortment of machineguns, Gatling guns, and missile launchers giving them a much more menacing appearance then their smaller brothers

In the skies, a pair of DINNs flew long range reconnaissance, machineguns and missile launchers at the ready.

Four TMF/A-802 BuCUE, 2 armed with railguns and 2 with missile launchers, stood next to the bipedal GINNs giving the appearance of a pack of hounds ready to be set loose on the hunt. And supporting them was a single _Lesseps_-class land battleship with two TFA-2 ZuOOTs acting as additional gun turrets.

At the forefront of the mobile suit contingent stood the custom GINN of the ace pilot Un No, its light brown colors easily distinguishable amongst its fellows with only a Gerbera Straight katana and a Tiger Pierce wakizashi strapped to its side for weapons, its pilot waiting to fight against the threat to his homeland in honorable combat.

The size and variety of the gathered ZAFT forces was large enough to make any possible invading OMNI Enforcer troops think twice before attacking. But it did nothing to intimidate their coming foe.

As if daring the human's machines to try and impede it, the Third Angel, easily twice the size of the largest of the present mobile suits, erupted from the ocean in a great plume of water. No sooner was it visible then every single long range weapon opened up on the monster. High-velocity projectiles from the linear tanks and rail gun equipped BuCUE whistled through the air towards the Angel. Missiles impacted against its hide. And heavy artillery attacks struck it from the land battleship and ZuOOTs.

Sachiel just shrugged off the attacks with its AT field, with the high powered attacks leaving no visible damage. After the fist volley's smoke cleared, the Angel retaliated. It eyes glowed as it fired a powerful blast of energy that took the shape of a cross as it struck its target. That single blast wiped out a significant portion of the assault vehicles and two GINNs that had been too close to the road.

With one obstacle out of the way, the Angel continued forward towards its goal, completely ignoring the continuing fire from the minor pests, even occasionally unleashing another energy blast that would force the mobile suits to retreat or be demolished. While the mechanized men had the mobility to avoid the energy attacks once they came to expect them, most of them were not fast enough to escape completely unscathed.

As it reached the shores, long range artillery ceased in favor of new tactics. The new assault was lead by Un No. With a thruster-enhanced leap, his GINN rocketed towards the Angel, katana held ready to slash the Angel in two.

Sachiel may be a large lumbering mass of destruction that dished out raw power to get what it wanted, but never let it be said that the Angel couldn't fight close up. Using its left arm it blocked the sword, the AT field preventing the blade from slicing into its skin. Then Sachiel reared its right fist to bash the machine's head in…had the GINN stayed there.

But Un No wasn't an ace for nothing. Backing off in time to avoid the punch, he let the rest of the GINNs open fire with their machineguns.

The damage done to Sachiel from the bullets was negligible, but it was starting to grow annoyed. Continuing forward, clearly not distracted from its goal, Sachiel shifted weapons, extending an energy lance and slashed it across an Assault GINN's torso. Another lance pierced a BuCUE that had ramped off a nearby hill in an attempt to smash the Angel into the ground with its body. The mobile suits fell back, one by one, as they attempted to stop the Angel from reaching the nearby city of Tokyo-2 while doing their best to avoid getting killed.

* * *

"We're sorry, but due to a state of emergency in the Kanto and Tokai regions all phone lines have been disconnected. Please hang up and seek the nearest shelter." Shinji sighed and hung up the phone.

'_What state of emergency?_' Was the question on the teenager's mind as he waited for his late pickup ride. '_Has the EA launched an invasion? Unlikely. With the recent offensive in Taiwan they would be consolidating their resources to protect the mass driver in Kaohsiung. And didn't the radio on the train announce that the ceasefire is back in effect? A typhoon perhaps?_'

While Shinji went over the possible list of why the city was deserted, and trying to think of a plausible explanation as to how he missed the memo, he caught something in the corner of his eye. Turing to get a better look, he saw a girl about his own age standing in the middle of the street. A coordinator, if her hair and eye color was anything to go by.

There was something about her alabaster skin, ruby eyes, and blue hair that caught Shinji's attention and wouldn't let go. At least not until something disturbed a nearby flock of birds. They flew off from their perches with various screeches of indignation. Shinji, startled by their sudden departure turned his head for only a second, but when he turned back the girl was gone as if she had never even been there.

'_Weird._' Thought Shinji, but before he could contemplate on the matter an explosion rocked the Earth. His theory of an invasion suddenly seemed _much_ more plausible. But his theory changed from invasion by the EA to a different sort of invasion as from around a small mountain stepped the massive form of a monster that was clearly not of this planet.

'_What is that!? What Is That!?_' The monstrosity was twice the size of a mobile suit, as evidenced by the GINNs zooming around on Guul subflight lifters and the aerial DINNs. The mobile suits were keeping up a steady stream of gunfire on the giant, but the bullets just seemed to bounce off its hide without leaving even a scratch.

When that didn't seem to work, a new GINN equipped with an M66 Canus short-ranged guided missile launcher flew in. It didn't even take a second for Shinji to realize the pilot's intentions, and it took that no longer for the young boy to start sprinting in the opposite direction. The GINN fired one of its missiles. The giant in turn countered by snatching the end of the explosive in one of its massive clawed hands. That seemed to be what the pilots of the mobile suits were waiting for as the GINN launched the rest of its missiles, followed by a barrage from the DINNs.

The force of the explosion was massive and the wind picked Shinji up, sending him flying several feet before bouncing back against the ground and hitting his head against the curb of the road. He laid there dazed for several seconds. When he came to, his eyes widened in horror. Thanking the wonders of science for his Coordinator reflexes, Shinji swiftly rolled up onto his feet and ran, narrowly having avoided being crushed by a GINN's severed arm, and right before the giant's foot came down and smashed it to pieces.

Shinji was trying to get as far away from the battle as possible, but logically he knew that to be impossible. He was right in the middle of a war zone and it would take hours to make it to safety on foot. However it seemed someone was watching out for the young Coordinator that day as Shinji heard the squealing of tire wheels as a blue Renault Alpine barreled down the street before it skidded and spun to a stop beside him.

"Get In!" Shouted the female driver as she opened the passenger door from the inside.

Shinji obeyed the command and jumped in. The woman he quickly recognized from a photo as the person who was supposed to pick him up. But instead of wearing a revealing tank top and cut off shorts, she wore a ZAFT green coat uniform and a captain rank insignia. Slamming her foot on the accelerator, the captain sent the car speeding away before he could even get the door properly closed.

The car raced down the street at a harrowing speed with the woman keeping her eyes on the battle behind them, somehow making every turn without even looking forward. Once she determined that they were far enough away, she turned to her passenger, without slowing down, and introduced herself. "Hello, Shinji Ikari. I'm Captain Misato Katsuragi. Sorry I'm late."

* * *

**Tokyo-3, Geo-Front, NERV Headquarters, Central Dogma**

Deep beneath the ground, within one of the most heavily fortified positions ever built by man on Earth, was the fortress called NERV. Sitting on an overlook within the bridge of the command center Central Dogma were three ZAFT military officers, their purple coats signifying each one as a General.

"Damn It!!"

And they were not happy.

"We're throwing everything we have at it and the thing is barely being slowed!" Cried General Ishimora in frustration.

Next to him, General Tonne sighed in resignation at the destruction. "Over the course of hours it's done more damage to our forces then the EA does in a week. If this keeps up we may have to resort to our trump card."

"_Are_ _you mad_!?" Shouted General Nakimura. "If the Atlantic Federation and the Eurasian Federation were to learn that we developed such a weapon…"

"They'll do nothing." Interjected Ishimora. "They know the danger the Angels pose to all of mankind and not even the most diehard Blue Cosmos supporter amongst their leaders will be able to persuade the entire EA to ignore the ceasefire and continue the war. Especially when it seems that just one Angel is able to accomplish that which the EA could not over the course of 11 months of war."

"Well," spoke up the moderate voice of Tonne, "if it would be preferable to keep our ace in the hole hidden, then we could always call upon 'them.'" There was no need to elaborate that the 'them' he was referring to were the two men sitting on another overlook just beneath the Generals.

One was the Sub Commander of NERV Kozo Fuyutsuki, an elderly man born in the very early 1950's and whose former profession was as a university professor. Fuyutsuki stood in his usual spot on the bridge, just behind and to the left of his superior.

That superior is Gendo Ikari, Commander of the First Branch of NERV here in Japan, as well as the Supreme Commander for every branch around the world.

Gendo watched the visual feeds of the battle between the Third Angel and the ZAFT mobile suits. Admittedly it was a rather one-sided battle. Oh sure the various GINNs, DINNs, and other mobile suits were putting on a good show of attacking the Angel and then dodging the retaliatory attacks, but it was ultimately pointless. The weapons the military were equipped with were simply incapable of penetrating the Angel's AT Field.

Eventually the ZAFT Supreme Council will realize that only NERV and their Evangelions could defeat the Angel and then they would relinquish control to him. The only thing he had to worry about was whether or not Captain Katsuragi would be able to deliver the Third Child on time. But as long as he did arrive on time then everything would be fine, after all Unit 01 was different from the others. Shinji should have little trouble synching with the mighty shadow of Lilith.

Nothing could interfere with the scenario.

"Sir!" Shouted the green coat tech Lieutenant Makoto Hyuga to the peanut gallery of officers. "We have a situation."

At the moment the Lt was under the temporary command of the Generals and it was Ishimora who answered. "We already have a situation Lt Hyuga. You are going to have to be more specific."

"Sir, remember that large unidentified object we detected entering the atmosphere?"

"Yes, we sent a team to investigate its speculated landing zone to see whether it was related to the Angel or was merely some junk from the debris belt whose orbit deteriorated. What of it?"

"The team has reported back and it's not space debris nor is it related to the Angel."

"Then what is it."

"I think you should see the visual." Said Makoto as he called up a second window next to that of the Angel's progress. The holographic screen showed the sight of a ship the likes of which no one at NERV had ever seen before, and that the Generals of ZAFT had only heard about. The vessel was easily 420 meters long, painted a blazing white with a bit of red, hovered over the land, and its most distinctive features were the two leg-like extensions that jutted forward from the bow. The angle of the camera shifted revealing that the Third Angel was visible in the distance and that the legged ship was on a direct intercept course with it.

* * *

**Road between Tokyo-2 and Tokyo-3**

The Renault Alpine that belonged to Captain Katsuragi tore down the streets of Japan in a mad bid to as far away from Tokyo-2 and the Angel as the driver could get it on its route to Tokyo-3. But the driver, being a military woman couldn't help but be curious about how the ZAFT mobile suits were faring at holding off the Angel, even though she knew enough not to expect too much progress against it. Still her curiosity grew too strong and she gave in to it, good thing she isn't a cat.

Bringing her beloved car to halt at a portion of the road that was along a cliff and provided a decent view of the city and the area between it and the cliff Misato pulled out a pair of binoculars and started examining the situation. "Damn," she muttered as she viewed the current assault force run out of ammo and retreat from the battle. "I knew that conventional weapons had little chance against an Angel, but it's still hard watching our mobile suit pilots get their asses handed to them in such a way."

"Uh, Captain Katsuragi…" began Shinji, his eyes drawn to something else that had appeared on the edge of his vision.

"Please Shinji, call me Misato." Stated Misato who kept her eyes glued to the Angel.

"Misato what is that?"

"What is what?" Asked Misato as she started scanning the field. "What are you talking…Whoa!" She exclaimed as she found what Shinji was talking about.

It was a vehicle, a ship, the likes of which she had never seen before. The majority of its body gleamed pure white, like fresh snow, and the rest of its bright colors shined with intensity, creating a distinctive and highly noticeable pattern. From stern to bow the ship was over 400 meters long. It had wings and flew over the land yet was too low and did not move the way an aircraft does. And Misato's eyes almost bugged out as she saw two turrets extend from the top of the leg-like extensions.

"Those are beam cannons," whispered Misato. "But the only ships with those kinds of weapons are all up in space. What is this one doing down here?" Then a thought struck the military trained woman. "Is it going to engage the Angel? Would those weapons work?"

Misato's question was answered a minute later as each of the four barrels let loose a stream of high intensity energy, accompanied by two rounds from a pair of linear cannons, at the Angel which had stopped and turned to the newcomer. The projectile rounds bounced off the Angel's AT Field. But the energy beams hit the barrier of orange hexagons with barely a moment of delay before they passed through and struck their target.

The Angel howled in pain, four patches of smoking green flesh visible through Misato's binoculars, her full attention on the wounded giant.

Shinji, however, was more focused at the warship as two hanger doors opened up and a pair of catapults extended. Quickly pulling out a pair of spare binoculars he had spotted earlier Shinji watched as from the two cavernous hangers of the ship five mobile suits, unlike any he had ever seen, were launched. His jaw dropped as the gray suits suddenly shifted, each becoming a different color. Their sleekness, the distinguishing colors, the horned crests upon their heads gave each the impression of superheroes compared to the more soldier-like image of the GINN.

The first of the mobile suits to attack was the green and brown one equipped with two large guns, firing two blasts of energy.

That seemed to wake the stunned Angel up which immediately started moving to attack the mobile suit, only for a red, blue, and white suit with a red winged pack on its back to leap with tremendous speed across its path, firing off a quick succession of energy blasts from its rifle, distracting the monster from the slower artillery unit.

Using the distraction as an opportunity, a blue and white unit charged in from behind, pulling out a weapon that created a beam of pink light in the form of a sword, and struck the Angel in the back. In its rage, the Angel swung its arms and smashed them into the mobile suit. The mobile suit was launched backwards by the Angel's tremendous strength. It quickly used its thrusters to slow its movement, but not enough to keep it from crashing into the cliff wall beneath where Misato's car was parked.

Both passengers held their breath as they leaned over in their seats to look over the edge, expecting to see the mobile suit in a ruined mess. But to their astonishment, the mobile suit picked itself up and leapt back into the fray with no visible damage to show from the hit and subsequent crash it endured.

The Angel at this time was bearing down on the black mobile suit, clearly intending to trap it. Misato's and Shinji's jaws both dropped as the suit's color shifted back to its original grey, and then it completely disappeared from their sight.

"Where'd it go?" Asked Shinji looking around. His question was answered after only a moment when a beam of energy emitted from thin air struck the Angel from the right. The Angel would have retaliated against the newly reappeared mobile suit if it weren't for the warship attacking with its beam cannons again.

Once again, the Angel shrieked in pain as more of its flesh was burned away, but its priorities had become clear. The mobile suits' attacks were like a bee's sting compared to what the legged ship could do. And so in retaliation the Angel's eyes shined as it fired a burst of energy that erupted into a cross shaped flare as it struck against the ship's side.

Misato sighed as she figured the ship a lost cause. The mobile suits seemed like they could take a lot of physical punishment, but what could survive an attack like that? However, as the light faded, what she saw was not a burnt pile of scrap, but the whole and intact ship. Granted, it was rather worse for the wear with at least two of its engines offline and several melted and broken portions of the hull, but still operable and in fighting shape. Though Misato doubted it could take another hit like that.

That must have been on the mind of the pilot of the green suit as he docked his weapons together and formed a large cannon that when it fired looked as powerful as any warship mounted weapon. The attack was easily enough to distract the Angel and allow the wounded ship to limp away to a safer position.

Speaking of a safer position, as Misato saw the ship retreat she suddenly remembered her duty and charge. "Ack! We're going to be so late!" She cried as she put the pedal to the metal and started tearing up pavement.

Shinji for his part continued to stare out the back window as the five mobile suits continued their attack against the Angel. "Amazing." He whispered as he watched the red suit assault the Angel with the four beam sabers attached to its limbs.

* * *

**Central Dogma**

"Yes sir. I understand sir." Said General Nakamura to the person on the other end of the phone line. Setting the phone down on the hook the General sighed. "We have been ordered by the Supreme Council to transfer all command over to NERV."

"What1?" Exclaimed General Ishamora. "How can they order that when the Angel has finally been stalled?"

"It's because the Angel has only been stalled," said General Tonne in a calm voice that belied his irritation. "Isn't it, Nakamura?"

"Yes, despite the appearance of the Legged Ship and all five G-Weapons whose weapons actually seem to hurt the Angel, all they've done so far is succeeding in stalling it. They have yet to deliver a killing blow, and at the rate the Angel is regenerating from the wounds inflicted, it is believed they never will. So command of the operation will be turned over to NERV. Don't disappoint us, Ikari." That last part was said to the Commander of NERV who had risen from his seat to face the Generals.

The man unconsciously adjusted his glasses as he brought his gaze to the three men that sat above him, not letting them see the bit of worry he had felt when the 'G-Weapons' appeared and started fighting the Angel and were shown capable of holding it off. "Of course not. After all this is why NERV exists."

* * *

**Highway between Tokyo-2 and Tokyo-3**

Half an hour later with the now slowly advancing Angel no longer visible in her review mirror Misato picked up her phone and made a call into NERV. "This is Captain Katsuragi reporting in that I have the Third Child and we are returning to base. We should be there in five minutes… Don't worry his safety is my top priority…I'd like a train prepared. An express of course… Say, Ritsuko, you wouldn't happen to know anything about that ship and those new mobile suits attacking the Angel? …Nothing? Not even a rumor? …G-Weapons? Never heard of it… Alright see you soon." Hanging up her phone Misato turned her attention to her passenger. "Shinji, do you have the ID your father sent you?

Shinji's response was to pull out the large business envelope that had been mailed to him, from which he extracted several official looking documents, Misato's picture, and finally a card with his photo and the logo for NERV on it. Seeing the card, Shinji was reminded yet again that it had been years since he had seen his father, and how little he knew about the man. "NERV. Is that my father's organization?" He asked the driver, not really sure of the answer despite the evidence.

"You mean you don't know what your father does?"

Shinji shook his head. "Not really. I mean I always figured that it had something to do with the military, and my teacher told me that it was important for the future of mankind."

"Teacher? Do you mean your guardian? He was a military man**,** wasn't he?"

"Yeah, he was a Colonel. We moved around a lot until he retired four years ago. During that time it was considered too troublesome to constantly transfer me into a new school if I wasn't going to stay there long so he decided to home school me."

"Wow, sounds tough. Bet you had a real hard time making friends."

"It wasn't that bad." Misato noticed that Shinji wasn't exactly very quick to explain why it wasn't that bad. And judging the way his eyes cast downward and the tone of his voice he was merely saying it, with no real feeling behind the sentiment.

As the two had been speaking Misato had since driven her car into a special garage and was now moving on a large set of tracks that was carrying the car and its occupants downward. When the tunnel ended, it opened up into the stunning vista of a lake surrounded by a forest in a massive metal dome, indicating that they were within an artificial cavern. "Whoa," breathed Shinji, stunned at the site, "a real Geo-Front."

"That's right." Said Misato, glad that her temporary charge's spirits were lifting at the breathtaking view. She pointed out to the right and downward where a large black pyramid stood. "And that is the secret headquarters of NERV, a man-made fortress against the Angels, and our last hope for humanity."

* * *

**Tokyo-3, Geo-Front, NERV Headquarters**

"Yeerrgg! This is why I hate wearing skirts in this place." Complained Misato as the change in air pressure from the opening of the automated doors caused her uniform to flutter about.

Shinji chose not to comment, instead keeping his nose in the NERV booklet that Misato had given him so that he could familiarize himself with the what the organization is and its purpose. It was filled with flowery speeches and technical data. In other words it was all glitter and no substance.

Bringing his eyes up from his current page Shinji was struck by something odd about his surroundings. "Uh, Misato haven't we been by here already? Twice?"

"Uh, it's just your imagination. This place is built like a maze and a lot of the corridors look the same." Misato patted herself on the back for the clever excuse.

Too bad Shinji didn't buy it. "You're lost, aren't you?"

"Shut up!" Discreetly Misato pulled out a map and started using it to navigate. '_I thought for sure that I finally knew my way around here. Oh I better hurry before someone calls Rits._' Alas for the poor Captain, she was a little too late to hope for such a thing. By the time she finally managed to navigate herself and Shinji to the elevator of her destination, the blond doctor was already there waiting inside.

"Uh, heh heh. Hey Ritsuko." Said the Captain sheepishly when she saw the head scientist of Project E, who wore…unusual attire.

"Honestly, Misato, I would have thought that you would be able to memorize the layout of where you work by now." Said the doctor as she moved aside to allow the other two to enter. Redirecting her gaze downward she gave the rather timid looking Shinji a once over. "So this is the Third Child," she said.

"Yup," confirmed Misato. "Delivered safe and sound just as I promised. So Rits, you sure you don't know anything about that ship and those mobile suits?" Asked Misato.

* * *

The three had long since left the elevator and were now on a platform that was moving up and diagonal.

"Weeell," began Ritsuko, "that was all I knew on the phone. However since then I was able to hear a few things from some people who keep their ears to the ground."

"Ooooh, do tell." Encouraged Misato.

"Scuttlebutt has it that the Generals were conversing about those machines and apparently they aren't exactly ZAFT military."

"What!? If they're not ZAFT machines**,** then whose are they?" Ritsuko didn't bother to answer as the truth came to Misato after a moment. "They couldn't be, they're OMNI? The Earth Alliance has mobile suits?"

"If what I heard is accurate, then those mobile suits, the 'G-Weapons,' are prototypes the EA built and that ship, which was referred to as the 'Legged Ship,' is the carrier created for their use. All built as part of a secret project."

Misato whistled. "Those machines were using mobile suit-sized beam weapons, Shinji and I even saw one of them get smacked by the Angel, smash into a cliff wall and walked away none the worse for wear. And another that could turn invisible. Considering that ship into the equation and it would look like the EA just pulled into the lead concerning technology. What's going on? Since when does ZAFT rest on its laurels when it came to technology?!"

"Don't know, but there's something else. I don't know what but the Generals know something that they're keeping quiet about."

"Well, whatever it is, all I can say is that I am glad that the ceasefire is back on and that whoever is commanding that ship decided to give us a hand. I feel like our chances for beating this thing and coming out alive are a lot better now. By the way, how is Unit 01 coming?"

"It is currently undergoing refrigeration using the C-type equipment." Informed Ritsuko casually.

"The C-type equipment?" Questioned Misato. "I thought we didn't have the funding to build it."

"We don't with our current budget." She growled with a deep scowl on her face. "In order to make the C-type equipment, I had cannibalize parts from the armor and the weapons of the A-type testing equipment and the spare B-type armor. All I was able to make was one set of the C-type equipment, and even then it's not up to spec! _How do they expect me to build weapons to kill Angels if I don't have the proper funding?!_" By the end of that little triad Ritsuko was a little out of breath. She glanced over at her now scared companions, one of whom was cowering behind the other and that was because she knew what the doctor was capable of when upset. "Uh, sorry about that, I tend to get a little emotional about what I can make with our_…limited_ budget."

* * *

Once they got off the escalator the three then proceeded to make their way across an amethyst lake via a motorized raft. Their destination, a large metal container. The interior of the container was dark. So dark that Shinji wouldn't have been able to see his own nose if it hadn't been for the square of light pouring in from the open door, and when that closed it became pitch black.

The lights of the container snapped on and Shinji couldn't stop himself from jumping in shock at the sight of the giant horned face directly in front of him. "A giant mobile suit?!"

"Not quite." Stated Ritsuko proudly. "While it shares many of the same technologies with mobile suits, this is a synthetic life form that was designed and created specifically to combat and defeat the Angels. This is the ultimate fighting machine: Evangelion Unit 01."

Shinji calmed down a bit, even depressed a little as he realized something. "This is what my father has been working on, isn't it?"

"Correct." The answer did not come from the two women, but rather from above them, where Gendo Ikari stood in an observation booth, looking down upon his son. "It's been awhile Shinji." The man said as a form of greeting to the child he hadn't seen in three years before turning his attention to the NERV personal. "We're moving out."

"Moving out!" Exclaimed Misato. "But Unit 00 is in cryostasis, and Unit 02 is in Germany!" It seemed impossible for NERV to move out with both of their active Evas unusable. Then Misato understood Gendo's intentions as if she was hit with a bag of bricks. "Wait! You're going to use Unit 01!"

"There is no other choice." Said Ritsuko, clearly pre-informed and prepared for this course of action.

"But Rei is in no condition to fight! We don't have a pilot!" Argued Misato.

"We just received one." Countered Ritsuko.

"You can't be serious!"

Ritsuko ignored that last comment in favor of turning to Shinji and said in a completely neutral tone. "Shinji Ikari, you will pilot Unit 01."

"But even Rei Ayanami took 11 months to synchronize with her Eva! It's impossible for him to do it, he just got here!"

"But if he can, Misato, if he can gain even the smallest synchronization ratio with the Eva, then we have a chance. And defeating the Angels is our top priority, no matter the risk." Returning her attention to Shinji, she asked the key question. "Now, Shinji, will you pilot?"

"I-I can't operate a machine like that." Was Shinji's shaky answer.

"But you can," Gendo countered coldly. "The Colonel did teach you how to pilot mobile suits, did he not?"

"Y-yes." Shinji's guardian had taught him how to pilot a mobile suit using simulators that, being a Colonel, he had easy access to even once he retired. In fact Shinji logged in as many, if not more, simulator hours as most recruits fresh from the training.

"Then," continued Gendo, "you should have little difficulty in controlling the Eva."

That may have been true but the thought of piloting anything in order to fight, especially against a monster like the Angel, filled Shinji with fear. "Can't you bring in a veteran mobile suit pilot if the Eva is so much like a mobile suit?"

"Impossible," said Dr. Akagi. "What makes Eva different from a run-of-the-mill mobile suit, what gives it the power to fight the Angels, also makes it impossible for an ordinary person to pilot it. Only a unique person born after Second Impact can activate an Eva and pilot it."

"Shinji," began Misato, kneeling down slightly and placing a hand gently on his shoulder, "I know this seems scary, and I don't like it either, but we need you. We need you to pilot Eva and fight the Angel, for the sake of everyone here. Please, will you pilot it?"

Making choices was not Shinji's strong suit, partially due to how the Colonel raised him to obey his superiors. But even if that wasn't the case, his personality was simply that of an indecisive person who let others decide for him. It was simply his way of dealing with people. Thus when confronted with such a choice, he became a stammering wreck.

After several seconds of watching his son's internal dilemma was enough for Gendo. With an unseen gesture he activated a monitor, showing the form of his Sub-Commander. "Fuyutsuki, wake Rei."

"Rei?" Gasped the old man. "Is she in any condition to pilot?"

"She's still alive, isn't she?"

The former professor merely nodded in resignation, after a few moments the monitor changed images to a black background with the words audio only.

"Rei."

"Sir?" responded a weak voice.

"Our spare appears to be useless. You will pilot."

"Yes sir," said the voice of Rei without any hesitation.

Gendo then turned his attention back to the trio below, where Shinji had yet to give an answer. "Enough," he said. "We have no time. Dr. Akagi, reconfigure Unit 01 for Rei." The command was reiterated by someone in a command booth somewhere.

Misato sighed and started walking away, knowing that with the issuing of the order she couldn't stay here and had to report to her post. Her counter**,** Ritsuko**,** did the same.

Shinji just stood there, in the middle of the walkway in front of the giant mobile suit known as Evangelion. His head bowed low in shame, his moment of usefulness having come and gone. '_I knew it. They didn't need me._' A door on the far side of the container opened and Shinji watched as several medical personal wheeled in the pilot. '_It's that girl!_' was Shinji's first thought. Then his eyes widened in shock as the girl he saw earlier that day was here and was a pilot. But the most shocking part was her injuries.

Bandages wrapped around her head and left eye, her right arm was in a cast, and other bandages were wrapped around her left arm and her torso, visible on the sleeveless portion of the skintight suit she wore. It didn't seem like she was taking painkillers as the simple act of sitting up left her gasping for breath.

'_She'll kill herself if she fights. I can't let her do it._' But before Shinji could voice this spark of courage the world shook as an attack from the Angel hit a weak spot in the Geo-Front's defenses. The quake threw everyone off their feet and Rei off her gurney.

In that moment several things happened, all happening beyond the scope of awareness. The first was the spark of courage roaring into an inferno for an instant and in the nanoseconds between Rei falling off the gurney to hitting the floor, Shinji tore across the room at a high speed before leaping, spinning mid-air, and catching the blue haired girl, acting as a cushion that protected her and prevented her wounds from opening.

The second was the damage the shockwave created, causing debris to fall from the ceiling, right above Rei's gurney

Shinji had spent too much time in his effort to catch Rei, and now not even his Coordinator reflexes could save him, not if he continued to protect the girl in his arms. Before anyone could react to save the two children**,** the eyes of Unit 01 glowed with power as its right hand broke free of its restraints**,** rising over the young Ikari. The metal debris bounced off the armored hand like pebbles.

"That's not possible!" Exclaimed Dr. Akagi, seeing but not believing what Unit 01 had done. "The Entry Plug hasn't even been inserted!"

Misato was less focused on the impossibility of what the Eva had done and was more focused on what could have caused it in the first place. The only plausible explanation she could think of was, "Did it move to protect something? To protect him? Eva's never responded to Rei this way."

Shinji didn't care what Unit 01 had done, even if he did file it away in the back of his mind. Instead he was focused on the blue haired girl in his arms. Seeing the pain Rei's injuries caused her, despite Shinji's efforts to save her from more pain, injuries undoubtedly related to piloting, strengthened Shinji's previous fear and threatened to drown the spark. Looking back at the possible source of pain Shinji found his spark of courage energy renewed. The power came from the Unit 01 whose eye glowed brighter with power, as if the monolithic beast was staring back at Shinji. Then something happened.

Shinji jerked slightly as he felt what could almost be called a burst of lightning flash through his mind. Instantaneously afterwards, he felt a strange sensation, familiar yet alien at the same time. It called out to him, telling him to pilot Eva.

"I'll do it! I'll pilot it!"

* * *

It didn't take long for NERV to get Shinji into the Entry Plug. The interior of the Entry Plug was almost the same as the cockpit of a mobile suit**,** so most of it was familiar. However some parts had been moved or slightly altered to accommodate the cylindrical shape of the Entry Plug. Once inside Shinji followed his training and pulled out the keyboard to start checking everything about the machine from O.S. to weapons to calibrations while technicians prepped the Eva.

"Calibration's zero moment point set at CPG. Control module connected to quasi-cortex molecular ion pump, flow rate normal. Meta-motor parameters set." Shinji let out a sigh as he finished checking over the system. "I really hope everything will work properly. I don't know what parameters an Eva needs to be set for. Now to check weapons." His fingers danced across the screen and called up the list of Eva's equipment. "Weapons include a progressive dagger stored in the left shoulder pylon and a Magoroku-Exterminate Sword MK I? What kind of sword is that? Well I'll know soon enough." He said as he pulled up another schematic. "Battery is fully charged, operation time…_ten minutes?! That can't be right!_"

"_Sorry, Shinji, but it is._" Said Dr. Akagi over the radio. "_Eva is different from mobile suits and that is the best our current battery technology can do._" Then growled under her breath, "_Of course if I had a bigger budget to work with…_"

Before the good doctor could continue Misato interrupted. "_Is everything ready?_"

"_Just about._" Responded the tech Lt Aoba.

"_Flooding Entry Plug._"

At the command a yellow liquid started filling up the Entry Plug from the bottom. "Hey! What's going on!?" Shouted Shinji fearfully just as the liquid rose past his head.

"_Don't worry. It's LCL and it's oxygenated so when it saturates your lungs it will supply oxygen directly to your blood._" Explained Ritsuko. "_It also helps to increase your synchronization level with the Eva. When the Eva activates your mind will be directly connected to it, with the synch level indicating how strong the connection is. With a high enough synch level you can actually control the Eva's movements with your mind. However, as much as we would prefer to, we can't always rely on that system, which is why we added in the controls of a mobile suit. The LCL will also act like a cushion and help prevent injury in battle._"

'_It didn't do Rei much good._' Thought Shinji, his face bulging from contained air. Through the entire explanation he had held his breath and he could hold out for another minute or two, but he would need air eventually. Closing his eyes he took the plunge and released his pent up carbon dioxide before taking a huge gulp of LCL. "It tastes like blood." He complained.

"_Suck it up! You're a boy__**,**__ aren't you?_" Barked Misato. If Shinji had more of a spine he would have wondered whether to spend the energy to glare at the woman, as it was he simply went back to work of familiarizing himself with the Eva.

"_Connecting secondary contact._"

Shinji blinked in wonderment as the LCL suddenly lost its translucent yellow color and became perfectly clear, as if it wasn't there. Then the interior of the Entry Plug shifted and became a rainbow of colors as tiny sparkling lights similar, to hundreds of diamonds, shimmered about him. Finally Eva's cameras activated turning the Entry Plug's walls into a view screen of outside the Eva.

"_Bidirectional circuits are open. Synchronization ratio is at 41.3%. Harmonics seem to be normal._"

"_Incredible._" Breathed Ritsuko at the sight of someone bypassing the absolute borderline and actually synchronize with an Eva on their first attempt. "_I didn't think this was possible but he actually has a high enough level to control the Eva with his mind. Granted, it would respond sluggishly, but it's possible._" Turning to Misato she gave the OK.

"_Begin launch sequence!_" Commanded the purple haired Operations Director.

The Eva cage became a hive of activity as the primary locks, secondary locks, and safety restraints that held the purple titan in place were removed and the Eva was moved to the launch pad.

Once in place a series of doors opened up and cleared the path of the catapult. Everything was ready.

"_Eva Launch!_"

Just as in the simulations of catapult launches Shinji felt the G-forces push him into the seat as the Eva rocket upward, before jolting to a stop. It took Shinji only a moment to gather his bearings. This catapult entrance was on the edge of the city and not too far away was the Angel and two of the five mobile suits that had been fighting it. The red one and the red, white, and blue one, only the latter of the two seemed to have changed equipment. Instead of the winged red pack it now had a green pack that included a large cannon.

"_Are you ready Shinji?_" Asked Misato in a concerned voice over the radio.

"As I'll ever be." Responded the Coordinator.

"_Final Safety Locks Release!_" Misato shouted switching back over to Operations Director mode. "_Evangelion Unit 01 Move Out! Remember Shinji, you only have ten minutes of power. Use them wisely._"

As the locks released, freeing the Eva from the catapult, the Angel took notice and started moving towards Shinji.

* * *

**Cockpit of the GAT-X105 Strike Gundam**

Kira was breathing hard as he brought the Strike to a rest. He had been fighting for over an hour with only two short periods of rest when he brought the Strike in to recharge. That's what Nicol, Yzak, and Dearka were currently doing as he and Athrun in the Aegis ran interference with the Angel.

After the first engagement the battle had gotten repetitive. If the Angel started focusing on making its way towards its target then the Gundams engaging it would concentrate their fire on it. That would set the Angel off into a state of rage where it would start attacking the unit closest to it, then another suit would move in, attack, and draw the monster's ire, only for the process to be repeated until the Angel grew weary of the cat and mouse game and started moving again.

So far, all they had managed to do was slow it down without leaving any lasting or crippling damage, and the city of Tokyo-3 was drawing closer.

"_Kira, something is happening at the city._" Reported Athrun.

Kira called up a window that showed a close up of the edge of Tokyo-3 where what he recognized as catapult rails had extended out of the ground, heralding the arrival of something. That something was a purple horned titan. And as if a switch was been pulled as soon as the titan appeared the Angel lost its interest in the Gundams and turned its focus on the new arrival.

"What is that?" Wondered Kira.

His question was answered moments later by Miriallia from the CIC. "_Kira, Athrun, you are ordered to back off and let the Evangelion engage the Angel. Support it from a distance if you can get a clear shot._"

"_Eva?_" Questioned Athrun.

"_According to Captain Ramius, the Evangelion is a mobile suit designed specifically to fight the Angel._"

"_You heard her Kira, let's back off._"

"Alright," responded Kira as he moved the Strike back, but not by much.

* * *

**Eva Unit 01's Entry Plug**

Shinji's first action was to simply move Unit 01 several steps forward out of the catapult which retracted as he cleared it. Then he quickly double checked movement controls and parameters to make sure nothing was wrong. Everything looked fine. It was not time to fight.

The Angel took several steps forward itself before raising a clawed arm. Shinji saw the blade of energy pull out from the elbow and his memory flashed back to the hapless GINN from earlier. The energy blade arced forward, extending incredibly over half a kilometer at tremendous speed. Shinji countered by ducking the Eva down and to the right barely avoiding the attack. However this attack, however close, was fortuitous for Shinji as his desire to be safe and protected at the moment allowed him to unconsciously deploy the Eva's AT Field.

"_Shinji,_" called Misato, "_your AT Field is deployed. Once you get close enough it will neutralize the Angel's AT Field, stripping it of its most powerful defense._"

"Right." Going offensive Shinji brought the Eva out of its crouch and into a running charge, getting past the Angel's defenses and smashing it with a pulverizing punch. The force of the impact sent the Angel stumbling backwards several steps, but it regained its balance. Taking advantage of his stunned foe**,** Shinji brought Unit-01's hand to the right shoulder pylon from which he extracted the katana shaped Magoroku-Exterminate Sword MK I, or Magoroku-E Sword for short. Activating the blade he swung it at the Angel.

The Angel blocked the weapon with its arm, only to shriek in pain as the oscillating blade started digging into the flesh and slowly cutting through the arm. Doing the only thing it could, the Angel fired a cross blast at point blank range, damaging itself as the Eva was flung backwards from the force before crashing into a building.

Shinji groaned as picked himself up. Looking at the Magoroku-E Sword he found that it had broken in the attack, with half of it still protruding from the Angel's arm. He couldn't tell if he was imagining Dr. Akagi's screams of horror emitting from the speaker or not, but it didn't matter as the Angel was bearing down on Unit 01 intent to finish it off.

Then, from behind the Angel, came movement. The white mobile suit had moved behind the Angel and targeting it with its cannon. Before the Angel could reach Shinji, the mobile suit fired, its weapon unleashing a surprisingly powerful stream of energy, striking the Angel from behind.

Without its AT Field, the Angel felt the full brunt of the hyper impulse cannon's attack and it let the world know with its shrieks and flailing limbs as bit by bit its body was burning away.

Shinji watched in awe before Misato came back with advice. "_Shinji, strike the core. If the core is destroyed then the Angel will die._" Knowing that this was his best chance Shinji pulled out the progressive dagger and leapt forward in an all-out charge. Adrenaline slowed Shinji's perception of time as he ignited the Eva's thrusters to increase the force as he drove the point of the dagger at the red core. The mobile suit's attack had already caused a series of spider web stress cracks to spread throughout it. As such the core could only resist the attack for all of a moment before it gave way, the progressive dagger's point plunging inward all the way to the hilt.

The attacks ended, with most of the Angel's torso burned away, and the only thing keeping it upright being the dagger held by the Eva, until Shinji dropped it. What was left of the Angel dropped unceremoniously to the ground as the Eva lowered itself to rest on one knee and the mobile suit's color shifted back to the dull grey from before.

Shinji felt drained as the chemical rush from earlier started to fade. Actual combat, he discovered was a _lot_ more draining then the simulation. After the day he had, all Shinji wanted to do was sleep. But there was something he had to do first. He directed Unit 01's head so that it directly faced the mobile suit and over an open channel said, "Thank you." With that he leaned back against the pilot's seat, closed his eyes and drifted away to the peaceful oblivion of sleep.

* * *

**Strike Cockpit**

"_Thank you._"

Kira paused as he heard the voice. It was a message directed to him from the Eva's pilot, but that couldn't have been right. The pilot sounded younger then he was.

"_Kira,_" called Athrun, "_Let's return. Nothing more for us to do here._"

"Yeah," agreed Kira as he turned the Strike to the approaching form of the _Archangel_. But he promised himself that he would find out who that pilot was.

* * *

**Central Dogma**

Misato sighed in relief as she leaned against a wall, letting it support her weight. One Angel down, so many more to go. But now she knew that there was real hope of beating them and not just the hope of having hope that she and everyone else at NERV had.

"Makoto," she said to one of the techs, "I want it logged that the defeat of the first Angel was a joint kill**,** split evenly between Shinji and whoever was piloting that unidentified mobile suit."

* * *

_**Archangel**_**, Cafeteria**

**February 12, 15 C.E.**

Morning had come after the Angel battle and the _Archangel_ could be found docked at a makeshift port at the ZAFT military base located on the edge of Tokyo-3. Scaffolding had been erected around the ship and the crew's technicians were busy at work repairing the damage from the emergency reentry and battle from the previous day. ZAFT had offered the _Archangel_ a spot to rest and resources for repairs, but no one aside from technicians were allowed off the ship without permission and only under guard. They had also offered to help with the repairs but Murrue turned them down.

Currently most of the crew who was not on duty was in the cafeteria grabbing a bite to eat. Among them was Kira's friends from Heliopolis.

"So what happens now?" Asked Kuzzey as he sat down with his breakfast.

"Don't know." Responded Sai as he nursed some coffee. "But I expect that there will be quite a few reprimands ready for the entire crew when we're finally back with the Alliance."

"How can you say that?" Asked Miriallia. "Won't they be glad for what we did?"

"Not necessarily," responded Sai. "Sure**,** we may have helped to take down that 'Angel' but in doing so we openly disobeyed our orders to join up with the 8th fleet. Not only that**,** but we overstepped our bounds by entering into an unauthorized alliance with members of the ZAFT military, and allowed ZAFT pilots and mobile suits aboard a highly classified Earth Alliance warship. Under ordinary circumstances we would be lucky to only receive a dishonorable discharge."

To this**,** Tolle said, "But we're not under ordinary circumstances. Earth was just attacked by some sort of giant alien monster. If we didn't do what we did then who knows what could have happened."

"Yeah," Kuzzey agreed quietly, "but what about that Eva of NERV's? The Angel was defeated minutes after it deployed. Maybe they didn't need our help after all?"

"Don't be too sure of that." The four friends turned to find the ZAFT pilot Dearka Elsman, food in hand, walking towards their table, Nicole Amalfi right behind him.

"Sorry for intruding," offered the green haired Coordinator as he sat down nearby with his own food. "We just wanted to grab a bit to eat before we finished prepping our machines to disembark."

"You're leaving?" Asked a surprised Tolle.

"Not that it's any of your business," said an approaching Yzak, who was only holding a small cup of coffee. "But we received new orders that the Le Creuset team is to be stationed here at the Tokyo-3 base as part of the Angel interception force."

"What did you mean earlier?" Miriallia asked Dearka.

Stopping in between bites Dearka explained. "What I mean is if they could have deployed that Eva any sooner than they would have. It _is_ the weapon created specifically to fight these Angels. A lot of lives and machines could have been saved if it had fought from the beginning. And I simply don't think they were able to. Pretty simple if you think about it. But there should be fewer problems now that we're stationed here to fight anymore Angels."

An uncomfortable silence dominated for the next few minutes as the Natural teens and the Coordinator teens ate their breakfast. Until Kuzzey asked a question that no one had thought of yet. "Has anyone stopped to consider where the Angel came from and how it got on Earth in the first place?"

* * *

_**Archangel**_**, Captain's quarters**

"I'd like to thank you two for seeing me so early." Said Lt Murrue Ramius to her two subordinates, Ensign Natarle Badgiruel and Commander Mu La Flaga.

"Not a problem**,** captain." Said Mu. "I always enjoy being in a pretty lady's room early in the morning."

"Commander!" Rebuffed Natarle.

"Hey**,** I'm just trying to lighten the mood." Mu defended.

Murrue cleared her throat to catch the two's attention. "Be that as it may," she began when she had it, "we're dealing with a rather serious matter here." Pulling out two sheets of paper she handed one to each. "These are copies of the _Archangel's_ new order received no more than an hour ago. Once we've completed repairs we are to head out to Panama and from there to JOSH-A (Joint Supreme Headquarters Atlantic) where we will receive a disciplinary hearing for our unauthorized actions."

Mu couldn't help but grimace, his normal good cheer temporarily dampened. "How bad is it going to be?"

"The hearing itself will be presided over by General Sutherland." Said Murrue with her own grimace, accompanied by Natarle and another from Mu. It was hardly a secret that William Sutherland was one of the highest members of the Atlantic Federation military who was also a member of Blue Cosmos. He may very well assert that their actions were open treason, if he had full control over the hearing and their punishment. "There may be a bit of good news. Admiral Halberton is coming down from space to participate. Since he was technically our commanding officer, how he feels about our actions will have a significant impact on what will happen to us. But there is one more important issue."

"Let me guess," said Mu. "It's about the kid right?"

"Yes," Murrue confirmed. "Considering his status as a Coordinator, a citizen of Orb, and an EA mobile suit pilot, the EA's only mobile suit pilot I might add, his situation is difficult to say the least."

"Where is Ensign Yamato?" Asked Natarle.

"He and that ZAFT Red, Athrun, went to go see the pilot of that Eva." Answered Mu. "Heard it took a few hours to get permission from NERV to enter their base's medical facilities where the pilot is sleeping off the fight."

* * *

**Holographic Emitter Room, Unknown Location**

In an undisclosed location known to but a handful of men stood twelve holographic monoliths. The monoliths were completely black in color except for the red letters that read SEELE, a roman numeral number to designate which is which, and Audio Only.

These monoliths represented the members of SEELE, the secret backers of NERV, the puppet masters of the Human Instrumentality Committee, and the men who control the UN. Their goals are known to only three others aside from their members.

Their meetings were never recorded, nor were their faces ever shown together in any way that could connect them aside from those who were also members of the Human Instrumentality Committee.

The topic of this meeting is the battle between Eva, the Third Angel, and the mobile suits known as the G-Weapons.

"This is inexcusable! This intervention was not described in the Dead Sea Scrolls!" SEELE 08 shouted angrily.

"To expect everything to go accordingly would be a disastrous mistake. This is why we need to leave room in the scenario for adjustments just in case of such a development." Said the calmer SEELE 11.

"The prophecy is only a prophecy because we have made it so. We enacted the requirements needed to awaken Adam and call his children and from there the Scrolls have set down the path humanity needed to take in order to defeat the Angels and progress in our evolution. But humanity is a creature of free will that we cannot control but guide." Stated SEELE 05.

"And our guidance would be unquestioned if it weren't for that accursed George Glenn." Growled SEELE 03.

There was a general consensus amongst the members of SEELE that if there was one man who had threatened their scenario more than any other, even inadvertently**,** it was George Glenn. Not only did they see his genetically enhanced Coordinators as a false evolution, but because of their impact on the world**,** many of SEELE's ventures were decidedly more difficult. Because of the creation of ZAFT, the Atlantic Federation, and the Eurasian Federation the United Nations had very little power, forcing the members of SEELE to rely on their private ventures more than they liked.

"This unexpected variable does not matter." Declared SEELE 01. "While it is true that these new mobile suits have generated a set of problems, they can be easily rectified. ZAFT and the EA will undoubtedly be focusing on producing beam weapons after seeing their relative effectiveness against Sachiel, so they will not have to rely on NERV and the Eva in the future. But the Fourth Angel Shamshel's capabilities will be very different from Sachiel's. And when it appears, the world will see why it needs NERV and the Evangelions. And if viewed in the proper context, this problem can also be counted as a blessing, for it can help clear an obstacle should Ikari become…problematic."

Murmurs of agreement rippled amongst the members of SEELE as they saw the potential advantage they could gain from this unexpected event.

"Still," spoke the voice of SEELE 02, who had a distinct French accent, "for the sake of preserving the scenario, it would be best if nothing happened to make the situation worse."

* * *

**NERV Medical**

Shinji walked the halls of NERV's Medical center on his way to visit Rei to make sure she was alright. Beside him was Misato who was going to take him to get his living assignment afterwards.

"Excuse me, are you Captain Misato Katsuragi?"

Turning around Shinji and Misato saw two young men in uniform walking up behind them. One of them wore a ZAFT red coat, the other in a blue Earth Alliance uniform.

"Yes," said Misato, "can I help you two?"

"Yes," said the one in the ZAFT uniform. "We were hoping you could show us to the pilot of the Eva, Shinji Ikari, ma'am."

"And you two are?"

The two saluted the superior officer as they gave their names and ranks.

"Ensign Kira Yamato, pilot of the GAT-X105 Strike Gundam."

"Lieutenant Athrun Zala, pilot of the GAT-X303 Aegis, uh Gundam."

Misato's eyes lit up in recognition. "Oh, you two must be pilots of those new machines. Can't tell you how grateful I am that you showed up, otherwise that Angel might have gotten us before we could get Unit 01 ready. As for Shinji Ikari, he's right here," she said indicating the boy next to her.

The two pilot's eyes widened in surprise as they took in the form of the meek 14-year-old. Kira's words probably summed up their feelings perfectly.

"A kid?"

* * *

**Author's Notes:** Well I hope this chapter was worth the wait. Hoped everyone enjoyed the Eva Gundam combo

A shout out to Tellemicus Sundance who not only challenged me to write this story but Beta'd this chapter and has been wonderfully considerate in allowing me to bounce ideas for the plot off him.

Now for some Extras

**Eva Equipment**

**C-type Experimental Combat Equipment:** Experimental Eva combat armor based on the standard B-type Equipment. The left shoulder pylon is equipped with a progressive dagger, a larger, more powerful version of the progressive knife. The right shoulder pylon is equipped with a back extension that houses the experimental Magoroku-Exterminate Sword MK I, also known as the Magoroku-E Sword or progressive sword. Finally the C-type has a mounted backpack with four thrusters to enhance jumps.

**ZAFT Military Command Structure**

I personally had trouble fully understanding the command structure of ZAFT in canon so for this story I created my own. The chain of command is separated into two categories Control Command and Combat Command.

**Control Command** rank structure is set up like the American military with Privates, noncommissioned officers, Lieutenants, Captains, Majors, and Colonels. The ZAFT Navy, both space and ocean, follow the same rank structure as the American Navy and command ZAFT's ships and subs. The characteristics of Control Command is that they all wear green uniforms with rank insignias and are the people who run military installations, but the commanding officer of the installation is given a black uniform to set them apart.

**Combat Command** is for field combat personal. Because Coordinators dominate the military ZAFT combat tactics focus more on highly skilled soldiers who can handle just about any situation. Soldiers trained in Combat Command are separated after graduation from the academy into Greens and elite Reds who were in the top of their class. Ranks for Combat Command are as follows, on the bottom is Ensign, followed by Lieutenants, then Captains, and finally Commanders are at the top and who wear white coats.

Commanders are in charge of field teams and task forces and are the equivalent of a Colonel. Their commands can even override the authority of officers in Control Command who are below Colonel unless their orders come from a Colonel or higher.

If members of Combat Command are assigned to a military base or ship and there is no Commander then they follow the orders of the installations/ship's commanding officer/executive officer.

Generals/Admirals can be promoted from either group and wear purple coats.

**Why ZAFT soldiers are working in NERV**

NERV sought the best and brightest to put in charge of their facilities and the Eva's so the majority of those in NERV are members of the military picked by NERV, given the opportunity, and volunteered to join.

**Joint Supreme Headquarters Atlantic**

The new JOSH-A. Since I couldn't have it in Alaska I decided to put it in an artificial facility built on the Northern coast of France in the middle of the English Channel which the Atlantic Federation has turned into a heavily fortified area with powerful defenses.

**Please Read and Review.**


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